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At least 559 records · Page 31

Ground-state degeneracy and complex magnetism of geometrically frustrated Gd 2 Ir 0.97 Si 2.97

We report a new triangular-lattice intermetallic compound Gd 2 Ir 0.97 Si 2.97 was successfully synthesized as single phase by deliberately introducing vacancies. Theoretical analysis suggests that the ground state is competing with several low-energy spin configurations due to magnetic frustration on a nearly ideal triangular lattice. Despite a number of competing magnetic states, the compound exhibits long-range antiferromagnetic order at16K, a long-range ferrimagnetic transition at 6.5 K, and a reentrant cluster-glass transition below T f ~ 3K. The complex magnetism in the compound could be correlated with competing antiferromagnetic and ferrimagnetic structures predicted theoretically.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Autonomous Tools for Attack Surface Reduction (Final Report)

The electric power grid is a complex critical infrastructure that forms the lifeline of modern society, and its secure and reliable operation is of paramount importance to national security and economic wellbeing. However, recent findings documented in authoritative sources indicate the threat of cyber-based attacks growing in numbers and sophistication. However, securing the grid against stealthy cyberattacks is a challenging task due to legacy nature of the infrastructure coupled with dynamic nature of threat landscape and ever-growing sophistication of the adversaries. Additionally, the grid’s attack surface continues to grow with the increased dependence on digital communications and control that now extends to each consumer through smart meters and distributed energy resources. Unfortunately, this expansive surface increases the grid’s vulnerability and further exposes critical control systems in both substations and control centers. To respond to this emerging need, we had successfully assembled an interdisciplinary team with academic- industry partnership to successfully conduct research, development, evaluation, demonstration, and commercialization of attack surface reduction tools, whose goal was to significantly reduce the cyber attack surface in the North American power grid. Our proposed project was a synergistic collaborative effort leveraging the synergistic expertise of the team members across power systems, cyber security and CPS security, testbeds, field deployments and demonstration, and successful commercialization. The following are the specific tasks that have been successfully completed two phases (2016-2020). Phase I: Task 1: Developed and implemented a robust Project Management and Data Management Plan, coupled with a well thought out Risk Mitigation Plan. Task 2.1: Developed a comprehensive framework that continually assesses and autonomously reduces the attack surface for the power grid control environment spanning across substations, control center and the SCADA network to significantly reduce the risks of cyber attacks. Task 2.2: Developed attack surface analysis techniques, metrics, and tools that assess the attack surface at multiple levels including the control center, substations, and the SCADA network. Task 2.3: Developed attack surface reduction techniques and tools that dynamically reduce attack surface and hence increase attacker’s cost without interfering in the critical functions of the system. Task 2.4: Prototyped, implemented, and quantitatively evaluated/validated the techniques and tools on a realistic industrial CPS security testbed environment by leveraging the unique resources of the team. Task 3: Developed Commercialization plan to transition the developed tools into power system industry stakeholders for a broader adoption by leveraging the expertise of our industrial members. Phase II: Task 4: Successfully completed field demonstration, verification, and evaluation of the effectiveness of the attack surface analysis and reduction techniques on a realistic utility testbed environment. This also involved the development of realistic scenarios, sound metrics, data sets, evaluation criteria, and documentation. Technology integration & Field demonstration: The project had significantly advanced the state-of-the-art research and practice in improving the cybersecurity of our nation’s power grid infrastructure against cyber threats. In particular, the proposed, designed, and deployed attack surface analysis and reduction algorithms and tools have contributed to significantly reducing the exposure and risk of the devices, substations, and the integrated SCADA/EMS/ DMS grid environment to cyber threat. Strong demonstration and evaluation techniques have verified the feasibility of the developed techniques on realistic cyber-physical testbeds and utility partner's real grid environment, and collaborative research and evaluation of attack surface reduction techniques (for wide-are monitoring and control) within a vendor (GE) EMS platform. The Attack Host Analyzer (AHA) tool that was developed through this project was made available through GitHub.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Optimizing Li‐Excess Cation‐Disordered Rocksalt Cathode Design Through Partial Li Deficiency

Li-excess disordered rocksalts (DRXs) are emerging as promising cathode materials for Li-ion batteries due to their ability to use earth-abundant transition metals. In this work, a new strategy based on partial Li deficiency engineering is introduced to optimize the overall electrochemical performance of DRX cathodes. Specifically, by using Mn-based DRX as a proof-of-concept, it is demonstrated that the introduction of cation vacancies during synthesis (e.g., Li 1.3-x Mn 2+ 0.4-x Mn 3+ x Nb 0.3 O 1.6 F 0.4 , x = 0, 0.2, and 0.4) improves both the discharge capacity and rate performance due to the more favored short-range order in the presence of Mn3+. Density functional theory calculations and Monte Carlo simulations, in combination with spectroscopic tools, reveal that introducing 10% vacancies (Li 1.1 Mn 2+ 0.2 Mn 3+ 0.2 Nb 0.3 O 1.6 F 0.4 ) enables both Mn 2+ /Mn 3+ redox and excellent Li percolation. However, a more aggressive vacancy doping (e.g., 20% vacancies in Li 0.9 Mn 3+ 0.4 Nb 0.3 O 1.6 F 0.4 ) impairs performance because it induces phase separation between an Mn-rich and a Li-rich phase.

25 ENERGY STORAGE↗

Synchrotron-based techniques for characterizing STCH water-splitting materials

Understanding the role of oxygen vacancy–induced atomic and electronic structural changes to complex metal oxides during water-splitting processes is paramount to advancing the field of solar thermochemical hydrogen production (STCH). The formulation and confirmation of a mechanism for these types of chemical reactions necessitate a multifaceted experimental approach, featuring advanced structural characterization methods. Synchrotron X-ray techniques are essential to the rapidly advancing field of STCH in part due to properties such as high brilliance, high coherence, and variable energy that provide sensitivity, resolution, and rapid data acquisition times required for the characterization of complex metal oxides during water-splitting cycles. X-ray diffraction (XRD) is commonly used for determining the structures and phase purity of new materials synthesized by solid-state techniques and monitoring the structural integrity of oxides during water-splitting processes (e.g., oxygen vacancy–induced lattice expansion). X-ray absorption spectroscopy (XAS) is an element-specific technique and is sensitive to local atomic and electronic changes encountered around metal coordination centers during redox. While in operando measurements are desirable, the experimental conditions required for such measurements (high temperatures, controlled oxygen partial pressures, and H 2 O) practically necessitate in situ measurements that do not meet all operating conditions or ex situ measurements. Here, we highlight the application of synchrotron X-ray scattering and spectroscopic techniques using both in situ and ex situ measurements, emphasizing the advantages and limitations of each method as they relate to water-splitting processes. The best practices are discussed for preparing quenched states of reduction and performing synchrotron measurements, which focus on XRD and XAS at soft (e.g., oxygen K-edge, transition metal L-edges, and lanthanide M-edges) and hard (e.g., transition metal K-edges and lanthanide L-edges) X-ray energies. The X-ray absorption spectra of these complex oxides are a convolution of multiple contributions with accurate interpretation being contingent on computational methods. The state-of-the-art methods are discussed that enable peak positions and intensities to be related to material electronic and structural properties. Through careful experimental design, these studies can elucidate complex structure–property relationships as they pertain to nonstoichiometric water splitting. A survey of modern approaches for the evaluation of water-splitting materials at synchrotron sources under various experimental conditions is provided, and available software for data analysis is discussed.

08 HYDROGEN↗

Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles

Bilayer vesicles that mimic a real biological cell can be tailored to carry out a specific function by manipulating the molecular composition of the amphiphiles. These bio-inspired and bio-mimetic structures are increasingly being employed for a number of applications from drug delivery to water purification and beyond. Complex hybrid bilayers are the key building blocks for fully synthetic vesicles that can mimic biological cell membranes, which often contain a wide variety of molecular species. While the assembly and morpholgy of pure phospholid bilayer vesicles is well understood, the functionality and structure dramaticlly changes when copolymer and/or carbon nanotube porins (CNTP) are added. The aim of this study is to understand how the collective molecular interactions within hybrid vesicles affect their nanoscale structure and properties. In situ small and wide angle X-ray scattering (SAXS/WAXS) and molecular dynamics simulations (MD) are used to investigate the morphological effect of molecular interactions between polybutadiene polyethylene oxide, lipids and carbon nanotubes (CNT) within the hybrid vesicle bilayer. Within the lipid/copolymer system, the hybrid bilayer morphology transitions from phase separated lipid and compressed copolymer at low copolymer loadings to a mixed bilayer where opposing lipids are mostly separated from the inner region. This transition begins between 60 wt% and 70 wt%, with full homogenization observed by 80 wt% copolymer. The incorporation of CNT into the hybrid vesicles increases the bilayer thickness and enhances the bilayer symmetry. Analysis of the WAXS and MD indicate that the CNT–dioleoyl interactions are much stronger than the CNT–polybutadiene.

59 BASIC BIOLOGICAL SCIENCES↗

Li-rich cathodes for rechargeable Li-based batteries: reaction mechanisms and advanced characterization techniques

Due to their high specific capacities beyond 250 mA h g -1 , lithium-rich oxides have been considered as promising cathodes for the next generation power batteries, bridging the capacity gap between traditional layered-oxide based lithium-ion batteries and future lithium metal batteries such as lithium sulfur and lithium air batteries. However, the practical application of Li-rich oxides has been hindered by formidable challenges. To address these challenges, the understanding of their electrochemical behaviors becomes critical and is expected to offer effective guidance for both materials and cell development. This work aims to provide fundamental insights into the reaction mechanisms, electrochemical challenges and modification strategies of lithium-rich oxides. We first summarize the research history, the pristine structures, and the classification of lithium-rich oxides. Then we review the critical reaction mechanisms that are closely related to their electrochemical features and performances, such as lattice oxygen oxidation, oxygen vacancy formation, transition-metal migration, layered to spinel transitions, ‘two-phase mechanism’, and lattice evolution. These discussions are coupled with state-of-the-art characterization techniques. As a comparison, the anionic redox reactions of layered sodium transition metal oxides are also discussed. Finally, after a brief overview of the correlation among the aforementioned mechanisms, we provide perspectives on the rational design of lithium-rich oxides with high energy densities and long-term cycling stability.

25 ENERGY STORAGE↗

Low-temperature domain-wall freezing and nonequilibrium dynamics in the transverse-field Ising model material CoNb 2 O 6

CoNb 2 O 6 is a rare realization of the transverse-field Ising model, making it a useful tool for studying both equilibrium and nonequilibrium many-body quantum physics. Despite a large body of work dedicated to characterizing this material, details of the ordered states in the presence of relatively weak transverse fields have not been discussed in detail. Here, we present a detailed study of CoNb 2 O 6 via ac susceptibility measurements in order to further characterize its low-temperature behavior in the presence of a transverse field. Specifically, we call attention to an unconventional freezing transition in zero field below T F = 1.2 K, occurring within the well-known commensurate antiferromagnetic (CAFM) state that onsets at T N2 = 1.9 K. We performed a series of transverse-field quenches into this frozen state, which resulted in a slowly relaxing susceptibility, χ' (t), that followed a logarithmic decay within the time range measured. Additionally, we discuss the frozen state in the context of the freezing of previously discussed “free” chains arising from domain walls between the four degenerate sublattices of the CAFM state. We also attempted to observe Kibble-Zurek scaling by quenching the transverse field into the frozen state at different rates. This produced a null result; the behavior can be fully explained by coarsening of domains over the time scale of the quenches. The absence of a clear Kibble-Zurek scaling is itself surprising, given the proposed ubiquity of the phenomenon for general second-order phase transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Extremely Overdoped Superconducting Cuprates via High Pressure Oxygenation Methods

Within the cuprate constellation, one fixed star has been the superconducting dome in the quantum phase diagram of transition temperature vs. the excess charge on the Cu in the CuO2-planes, p, resulting from O-doping or cation substitution. However, a more extensive search of the literature shows that the loss of the superconductivity in favor of a normal Fermi liquid on the overdoped side should not be assumed. Many experimental results from cuprates prepared by high-pressure oxygenation show Tc converging to a fixed value or continuing to slowly increase past the upper limit of the dome of p = 0.26–0.27, up to the maximum amounts of excess oxygen corresponding to p values of 0.3 to > 0.6. These reports have been met with disinterest or disregard. Our review shows that dome-breaking trends for Tc are, in fact, the result of careful, accurate experimental work on a large number of compounds. This behavior most likely mandates a revision of the theoretical basis for high-temperature superconductivity. That excess O atoms located in specific, metastable sites in the crystal, attainable only with extreme O chemical activity under HPO conditions, cause such a radical extension of the superconductivity points to a much more substantial role for the lattice in terms of internal chemistry and bonding.

Sederholm, Linda (ORCID:0000000172090509)↗

Specific heat and gap structure of a nematic superconductor: Application to FeSe

We report the results of our in-depth analysis of spectroscopic and thermodynamic properties of a multiorbital metal, like FeSe, which first develops a nematic order and then undergoes a transition into a superconducting state, which coexists with nematicity. We analyze the angular dependence of the gap function and specific heat C v (T) of such a nematic superconductor. We specifically address three issues: (i) the angular dependence of the gap in light of the competition between the nematicity-induced s - d mixture and the orbital transmutation of low-energy excitations in the nematic state, (ii) the effect of nematicity on the magnitude of the jump of the specific heat C v (T) at T c and the temperature dependence of C v (T) below T c , and (iii) a potential transition at T c1 < T c from an s + d state to an s + e iη d state that breaks time-reversal symmetry. We consider two scenarios for a nematic order: scenario A, in which this order develops between d xz and d yz orbitals on hole and electron pockets, and scenario B, in which there is an additional component of the nematic order for d xy fermions on the two electron pockets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Infinitely rugged intra-cage potential energy landscape in metallic glasses caused by many-body interaction

The absence of translational symmetry in glassy materials poses a significant challenge in establishing effective structure-property relationships in real space. Consequently, the potential energy landscape (PEL) in phase space is widely utilized to comprehend the complex phenomena in glasses. The classical PEL features a two-scale profile comprising mega-basins and sub-basins, corresponding to α-relaxations (e.g. glass transition) and β-relaxations (e.g. local cage-breaking atomic rearrangements), respectively. Recent studies, however, reveal that sub-basins are not smooth and contain finer structures, the origins of which remain elusive. Here we probe the smoothness of sub-basin bottoms in glasses' PEL by introducing small intra-cage cyclic loading and then measuring the net changes in atomic-level stresses. Compared to glasses with pair interaction, glasses with many-body interaction exhibit orders-of-magnitude larger and loading-dependent stress changes even before the first cage-breaking event takes place, which reflect much more feature-rich sub-basins. We further demonstrate this stark contrast stems from the spatial distribution of individual atom's constraining force field. Specifically, at vanishing perturbations, many-body interactions disrupt the positive-definite synchrony in energy variations of the perturbed atom and the whole system, causing inherently less confined atomic responses and infinitely rugged sub-basins. The implications of these findings for the selective addition or removal of fine structures in the PEL and the subsequent tuning of glassy materials' responses to external stimuli are also explored.

36 MATERIALS SCIENCE↗

Modeling Framework for the Assessment of a Sustainable Hydrogen Production and Supply Chain Network in California

The cost-effective and sustainable deployment of hydrogen supply and demand networks, especially in large economic regions like California, can be challenging considering the spatial-temporal availability and variability of the different actors across the network such as production processes, distribution modes, and end-users. In this presentation, we will provide an overview and demonstration of a modeling framework used to assess the environmental, economic, and human health impacts of plausible hydrogen production and supply chain networks in California. Scenarios focus on green hydrogen production pathways using water electrolysis and biomass gasification. End-use applications included in the model are transit, medium and heavy-duty trucking, port authorities, and power and aviation companies that currently consume natural gas, diesel, and aviation fuel for their day-to-day operation. Representative locations for hydrogen production and end-use are based on recent projections of the hydrogen economy in California. All mass and energy flows, as well as estimated emissions, are based on H2A process model designs and projections of technology performance, literature review, and LBNL process, economic and life cycle modeling, and not on company data for the sake of this presentation. Human health impacts are included following methodologies developed for the University of California Irvine HyDeal project. Life cycle phases associated with hydrogen production include feedstock preparation (water and biomass), energy production and consumption (renewable, grid, and combination of renewable and grid electricity), maintenance (chemical utilization in electrolysis and natural gas combustion in gasification), carbon sequestration, hydrogen storage (compression and liquefaction), and distribution (truck and pipeline). We apply the framework utilizing California specific emission factors, financial data, and human health damages and explore the impact of network characteristics on results. Example variations include: the inclusion of policy incentives or not, different representations of the electricity grid and source, electrolysis versus gasification versus combinations of both for production, liquefaction versus compression based on producer capacity cutoffs, transportation truck versus pipeline based on existing infrastructure, and ultimate end use. Comparison of these different scenarios can help inform future projects by demonstrating the trade-offs among environmental, economic, and human health impacts. This model, automated in R, is a starting platform upon which new analysis, modeling capabilities, locations, and emission factors can be rapidly tested and integrated.

Zaki, Mohammed Tamim↗

A Noncentrosymmetric Polymorph of LuRuGe

In this work, we report a new polymorph of LuRuGe, obtained in indium flux. This phase exhibits the noncentrosymmetric ZrNiAl-type structure with the space group $Ρ\bar 62m$ as determined by single-crystal X-ray diffraction. This polymorph can convert into another centrosymmetric polymorph (TiNiSi-type structure, space group Pnma ) at high temperatures. In this work, we performed electrical transport, magnetization, and specific heat measurements on this new phase. It shows metallic behavior with a Hall sign change from negative at 2 K to positive at 125 K. LuRuGe exhibits Pauli paramagnetism as the ground state with no local magnetic moments from either the Ru or Lu site. The Debye temperature Θ = 348 K and electronic coefficient γ e = 3.6 mJ K –2 mol –1 are extracted from the low-temperature specific heat data in LuRuGe. We also carried out first-principles density functional theory calculations to map out the electronic band structure and density of states. There are several electronic bands crossing the Fermi level, supporting a multiband scenario consistent with the Hall sign change. The density of states around the Fermi level is mainly from Ru 4d and Ge 4p electrons, indicating a strong hybridization between those atomic orbitals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Statistical distributions for transient transport

Here, this paper introduces the use of statistical distributions based on transport differential equations for clear distinction of transport modes within transient kinetic experiments. More specifically, novel techniques are developed for the transient data obtained through the Temporal Analysis of Products (TAP) reactor and are applicable to experiments where pulse response into a gas flow is used. The methodology allows distinguishing between two domains of diffusion transport in heterogeneous catalytic systems, i.e., Knudsen and non-Knudsen diffusion, using statistical fingerprints, and finding the transition domain. Two distribution parameters were obtained that directly result in coefficients that correspond to the concentration and the rate of transport. Using a linear relationship between the rate and concentration coefficients, Knudsen diffusion is revealed when the rate of transport is constant and non-Knudsen diffusion is confirmed when the rate of transport coefficient is a function of the concentration coefficient. As a result, accurate transport information can be extracted from experimental data even in the presence of comprising instrument drift or noise particularly when analyzing higher pressure pulse responses with complex transport. This enables more direct investigation of experiments influenced by gas-phase reactions.

TAP reactor↗

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

Modulating charge transport via 2 MeV He + irradiation in VO 2

Vanadium dioxide (VO 2 ) is of interest for adaptive electronic applications such as neuromorphic neuristor devices and variable emissivity or tunable thermal control materials, thanks to its key property—a metal–insulator transition (MIT) at 68 °C that is accompanied by a dramatic change in electrical and optical properties. To improve performance in these roles, it is critical to develop approaches to engineer transport properties and the MIT behavior. While many documented techniques exist to modulate the MIT and film resistivities via lattice strain and chemical doping, less is known about the effects of ion irradiation on the intrinsic properties of VO 2 , despite the ability to control the spatial distribution of irradiation beams and the prevalence of high energy ion implantation in the semiconductor industry. The impact of irradiation of different acceleration energies on the responses of VO 2 is of specific interest, as charged particle energy generally impacts both the resulting defect profile and corresponding transport behavior. Here, we demonstrate that 2 MeV He ions at equivalent calculated displacements per atom, in two different types of films, can create remarkable changes to the nature of charge transport in VO 2 , especially in the low-temperature insulating phase. Simulation of resulting changes in electrical conductivity reveals that He ion irradiation offers a strategy to increase both oscillation frequency and the signal transmission. These results provide insights into the intentional design of defect populations to modulate transport for neuromorphic VO 2 devices.

Gurrola, Rebeca M. [Texas A & M Univ., College Sta↗

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗

Combining Theory and Experiment to Map the Atomic-Level Structure–Energy Pathways of Adsorbate-Mediated Phase Changes in a Cooperatively Flexible Metal–Organic Framework

An important subclass of metal–organic frameworks (MOFs) exhibits cooperative flexibility, wherein individual crystallites undergo global structural phase changes in response to external stimuli. Where cooperative flexibility results in reversible changes between crystalline states of distinct accessible porosity, these frameworks can exhibit rare yet desirable behaviors that cannot be explained by local dynamics alone. Yet, the chemical and structural origins of cooperative flexibility and how frameworks undergo these reversible phase changes at the atomic level remain poorly understood. Deliberate design for specific applications is therefore exceedingly difficult, and there is great impetus to develop a fundamental understanding of this phenomenon. Here, an effective and widely accessible computational approach is developed, which is designed to provide microscopic resolution via direct comparison to experimental data along the desorption-guided pathway. The strategy is applied to explain the desorption-induced phase change in an experimentally well-characterized framework, CdIF-13 (sod-Cd(benzimidazolate)2), where experiment alone was unable to resolve the atomistically detailed phase change landscape. Our findings reveal that the cooperative phase change pathways are adsorbate dependent with thermodynamics of intermediate structural states dictated by a nuanced interplay of ligand orientation, skeletal symmetry, and modes of surface adsorption. The results reveal that this isotropically flexible framework is “chaperoned” through a complex energy landscape by specific adsorbates, revealed by the reported computational approach with atomic-level insight and validated by experimentally determined structures. Thus, this work facilitates both understanding and future design of flexible materials for applications in gas storage, transport, delivery, and separation technologies.

03 NATURAL GAS↗

Monte Carlo study of the pseudogap and superconductivity emerging from quantum magnetic fluctuations

Abstract The origin of the pseudogap behavior, found in many high- T c superconductors, remains one of the greatest puzzles in condensed matter physics. One possible mechanism is fermionic incoherence, which near a quantum critical point allows pair formation but suppresses superconductivity. Employing quantum Monte Carlo simulations of a model of itinerant fermions coupled to ferromagnetic spin fluctuations, represented by a quantum rotor, we report numerical evidence of pseudogap behavior, emerging from pairing fluctuations in a quantum-critical non-Fermi liquid. Specifically, we observe enhanced pairing fluctuations and a partial gap opening in the fermionic spectrum. However, the system remains non-superconducting until reaching a much lower temperature. In the pseudogap regime the system displays a “gap-filling" rather than “gap-closing" behavior, similar to the one observed in cuprate superconductors. Our results present direct evidence of the pseudogap state, driven by superconducting fluctuations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗